Just use Dop Mii to install any missing IOS files you may need - no need to worry about updating system menu (unless you want to). I am still on 3.2 and have no problems
quicky looking at that guide it does not seem to mention a cIOS or anything like that - and you need one of them to play from USB - take a look at http://gbatemp.net/t207126-nus-auto-downloader-for-windows
My apologies - as you are on 3.3 you do need to update in order to run start patch or priiloader to prevent disc updates as there are no hacks for that version of system menu. Follow the sticky guide to update your wii to 4.2 and then install priiloader or startpatch to block disc updates.
games do not require a specific version of system menu - just use a WAD Manager and install the IOS you need. Install priiloader and tell it to skip disc updates. I am on 3.2 and not found a game i cant run yet.
none of that should cause a brick and the chances are pretty slim - but possible - say you have a power cut ? thats the only main danger i can forsee, and I have installed bootmii as a boot2 on both my wiis and no bricks
could the pink fish disc strike again? if you could mod that to install IOS36 as well as the IOS16 it has within it you can then smash stack and run wad manager under 16
You dont need to update to 4.2 to get the shop working - just update the shop to v18 and get latest IOS61 and you can get back into the shop and download the iplayer
Twiser install the Homebrew channel to be able to see and run the NeoGamma app from your sd card and make sure they are in the apps folder eg sd:/apps/neogamma/boot.dol